Re: Performance degradation in PostgreSQL 7.1beta3 vs 6.5.3

"Robert E. Bruccoleri" wrote:

You can try starting postmaster with the "-o -fs" option. This will disable sequential scans if there is an index.
Thereis also an environment variable you can set, prior to the operation. I have run into this same problem.
 


> Dear Tom,
>         I am writing to you because you are the maintainer of the
> query optimizer and planner.
>         I have found a very significant performance degradation
> between PostgreSQL 6.5.3 and 7.1beta3, which will severely impact two
> large applications that I have developed and maintain for several
> clients.  The performance difference is seen with the use of indices in
> SELECT statements, whereby the current release does not make effective
> use of the indices and 6.5.3 does. All of these tests were run on a SGI
> R10000 Indigo2 system running Irix 6.5. All the regression tests passed
> as expected for both versions.
>         I have followed the discussion in pgsql-hackers over the previous
> months and others have noted some performance problems, and the response
> has typically been to VACUUM the tables. Unfortunately, this is not a
> practical option for my applications. They are very large -- I have one
> table that is 17GB in length, and the applications are used frequently.
> More importantly, PostgreSQL 6.5.3 works very, very well without
> VACUUM'ing.
>         In order to assist you to diagnosing and correcting this
> problem, I have prepared a test database that shows the problems. I
> will attach three files; the test script, the log from running it on
> version 6.5.3, and the log from running it on version 7.1beta3. In
> addition, I have setup an anonymous FTP directory on
> ftp.congen.com:/pub/pg_perf which contains all of these files as well
> as the compressed table dumps used to build the test database. (When
> you have finished copying the files, please let me know.)
>         The test script creates the database including the necessary
> indexing, and then runs EXPLAIN on each of the queries followed by
> actually executing the queries with "timex" commands to report elapsed
> times.  The striking difference in the query plans is that 7.1 uses
> only sequential searches for the SELECT's whereas 6.5.3 uses index
> scans. As a result, 7.1 is almost two orders of magnitude slower than
> 6.5.3 with exactly the same data, schema, and queries.
>
>         I plead with you to revisit this question of performance and
> fix PostgreSQL 7.1 to work as well as PostgreSQL 6.5.3 does. I depend
> upon PostgreSQL for much of my work, and I do not want to abandon it
> because of this performance problem which arose only recently. Thank
> you.
>
> +----------------------------------+------------------------------------+
> | Robert E. Bruccoleri, Ph.D.      | Phone: 609 737 6383                |
> | President, Congenomics, Inc.     | Fax:   609 737 7528                |
> | 114 W Franklin Ave, Suite K1,4,5 | email: bruc@acm.org                |
> | P.O. Box 314                     | URL:   http://www.congen.com/~bruc |
> | Pennington, NJ 08534             |                                    |
> +----------------------------------+------------------------------------+
>
>   ------------------------------------------------------------------------
> #!/bin/csh
>
> createdb perf_test
>
> gunzip <proteins.dmp.gz | timex psql -e perf_test
> gunzip <comparisons_4.dmp.gz | timex psql -e perf_test
> gunzip <concordance_91.dmp.gz | timex psql -e perf_test
>
> psql -e perf_test <<EOF
> explain select * from comparisons_4 where name1 = 'HI0001';
> explain select count(*) from comparisons_4 where code = 80003;
> explain select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 = 'HI0003' and c.name2 = p.name;
> explain select c.target_name, c.matched_name, c.score, p.purpose from concordance_91 c, proteins p where
c.matched_name= p.name;
 
> EOF
>
> timex psql -e -c "select * from comparisons_4 where name1 = 'HI0001'" perf_test
> timex psql -e -c "select count(*) from comparisons_4 where code = 80003" perf_test
> timex psql -e -c "select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 = 'HI0003' and c.name2 =
p.name"perf_test
 
> timex psql -e -c "select c.target_name, c.matched_name, c.score, p.purpose from concordance_91 c, proteins p where
c.matched_name= p.name" perf_test
 
>
>   ------------------------------------------------------------------------
> CREATE TABLE "proteins" (
>         "name" character varying(16),
>         "organism" text,
>         "start_position" int4,
>         "last_position" int4,
>         "seq" text,
>         "purpose" text,
>         "alternate_key" character varying(16),
>         "comment" text,
>         "compared" bool,
>         "complement" bool,
>         "chromosome" character varying(4),
>         "essentiality" float8);
> QUERY: CREATE TABLE "proteins" (
>         "name" character varying(16),
>         "organism" text,
>         "start_position" int4,
>         "last_position" int4,
>         "seq" text,
>         "purpose" text,
>         "alternate_key" character varying(16),
>         "comment" text,
>         "compared" bool,
>         "complement" bool,
>         "chromosome" character varying(4),
>         "essentiality" float8);
> COPY "proteins" FROM stdin;
> QUERY: COPY "proteins" FROM stdin;
> CREATE  INDEX "protein_names" on "proteins" using btree ( "name" "varchar_ops" );
> QUERY: CREATE  INDEX "protein_names" on "proteins" using btree ( "name" "varchar_ops" );
> CREATE  INDEX "protein_organism" on "proteins" using btree ( "organism" "text_ops" );
> QUERY: CREATE  INDEX "protein_organism" on "proteins" using btree ( "organism" "text_ops" );
> CREATE
> CREATE
> CREATE
> EOF
>
> real     1:11.42
> user        3.15
> sys         0.53
>
> CREATE TABLE "comparisons_4" (
>         "name1" character varying(16),
>         "name2" character varying(16),
>         "z_score" float8,
>         "expected" float8,
>         "local_overlap_ratio" float8,
>         "local_overlap_count" int4,
>         "overlap_ratio" float8,
>         "code" int4);
> QUERY: CREATE TABLE "comparisons_4" (
>         "name1" character varying(16),
>         "name2" character varying(16),
>         "z_score" float8,
>         "expected" float8,
>         "local_overlap_ratio" float8,
>         "local_overlap_count" int4,
>         "overlap_ratio" float8,
>         "code" int4);
> COPY "comparisons_4" FROM stdin;
> QUERY: COPY "comparisons_4" FROM stdin;
> CREATE  INDEX "comparisons_4_name1" on "comparisons_4" using btree ( "name1" "varchar_ops" );
> QUERY: CREATE  INDEX "comparisons_4_name1" on "comparisons_4" using btree ( "name1" "varchar_ops" );
> CREATE  INDEX "comparisons_4_name2" on "comparisons_4" using btree ( "name2" "varchar_ops" );
> QUERY: CREATE  INDEX "comparisons_4_name2" on "comparisons_4" using btree ( "name2" "varchar_ops" );
> CREATE  INDEX "comparisons_4_code" on "comparisons_4" using btree ( "code" "int4_ops" );
> QUERY: CREATE  INDEX "comparisons_4_code" on "comparisons_4" using btree ( "code" "int4_ops" );
> CREATE
> CREATE
> CREATE
> CREATE
> EOF
>
> real    16:42.13
> user        5.86
> sys         0.96
>
> CREATE TABLE "concordance_91" (
>         "target_name" character varying(16),
>         "matched_name" character varying(16),
>         "score" text);
> QUERY: CREATE TABLE "concordance_91" (
>         "target_name" character varying(16),
>         "matched_name" character varying(16),
>         "score" text);
> REVOKE ALL on "concordance_91" from PUBLIC;
> QUERY: REVOKE ALL on "concordance_91" from PUBLIC;
> GRANT ALL on "concordance_91" to PUBLIC;
> QUERY: GRANT ALL on "concordance_91" to PUBLIC;
> COPY "concordance_91" FROM stdin;
> QUERY: COPY "concordance_91" FROM stdin;
> CREATE
> CHANGE
> CHANGE
> EOF
>
> real        0.30
> user        0.02
> sys         0.04
>
> explain select * from comparisons_4 where name1 = 'HI0001';
> QUERY: explain select * from comparisons_4 where name1 = 'HI0001';
> NOTICE:  QUERY PLAN:
>
> Index Scan using comparisons_4_name1 on comparisons_4  (cost=2.05 rows=1 width=64)
>
> explain select count(*) from comparisons_4 where code = 80003;
> QUERY: explain select count(*) from comparisons_4 where code = 80003;
> NOTICE:  QUERY PLAN:
>
> Aggregate  (cost=2.05 rows=1 width=12)
>   ->  Index Scan using comparisons_4_code on comparisons_4  (cost=2.05 rows=1 width=12)
>
> explain select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 = 'HI0003' and c.name2 = p.name;
> QUERY: explain select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 = 'HI0003' and c.name2 =
p.name;
> NOTICE:  QUERY PLAN:
>
> Nested Loop  (cost=4.10 rows=1 width=36)
>   ->  Index Scan using comparisons_4_name1 on comparisons_4 c  (cost=2.05 rows=1 width=12)
>   ->  Index Scan using protein_names on proteins p  (cost=2.05 rows=36840 width=24)
>
> explain select c.target_name, c.matched_name, c.score, p.purpose from concordance_91 c, proteins p where
c.matched_name= p.name;
 
> QUERY: explain select c.target_name, c.matched_name, c.score, p.purpose from concordance_91 c, proteins p where
c.matched_name= p.name;
 
> NOTICE:  QUERY PLAN:
>
> Nested Loop  (cost=2093.00 rows=36840 width=60)
>   ->  Seq Scan on concordance_91 c  (cost=43.00 rows=1000 width=36)
>   ->  Index Scan using protein_names on proteins p  (cost=2.05 rows=36840 width=24)
>
> EXPLAIN
> EXPLAIN
> EXPLAIN
> EXPLAIN
> EOF
> QUERY: select * from comparisons_4 where name1 = 'HI0001'
> name1 |name2          |z_score|expected|local_overlap_ratio|local_overlap_count|overlap_ratio| code
> ------+---------------+-------+--------+-------------------+-------------------+-------------+-----
> HI0001|PDB2DBV_O      | 1217.4|       0|            0.56716|                335|     0.560468|30012
> HI0001|PDB4DBV_O      |   1207|       0|            0.56418|                335|     0.557523|30012
> HI0001|PDB2GD1_P      | 1226.4|       0|            0.57015|                335|     0.563423|30012
> HI0001|PDB1GAE_O      | 1861.8|       0|            0.83133|                332|     0.814164|30012
> HI0001|PDB4GPD_1      | 1357.8|       0|            0.64865|                333|     0.637169|30012
> HI0001|HP1346         |  850.3| 6.9e-41|            0.39222|                334|     0.386435|30005
> HI0001|TP0844         |  780.3| 5.8e-37|            0.46307|                352|     0.465716|30014
> HI0001|PDB1HDG_O      | 1020.4|       0|            0.48024|                329|     0.466074|30012
> HI0001|SCPIR-DEBYG1   | 1405.2|       0|             0.6497|                334|     0.640117|30000
> HI0001|Rv1436         |  970.4|       0|            0.49558|                339|      0.49558|30010
> HI0001|PDB1CER_O      |  949.7|       0|            0.47734|                331|     0.466075|30012
> HI0001|PDB1NLH_       |  935.1|       0|            0.46847|                333|     0.458825|30012
> HI0001|PDB1GGA_A      |    918|       0|            0.52125|                353|      0.51397|30012
> HI0001|PDB1GAD_O      | 1869.5|       0|            0.83434|                332|     0.817112|30012
> HI0001|PDB1GYP_A      |  900.1|       0|            0.51275|                353|     0.505589|30012
> HI0001|MG301          |  866.7|       0|            0.43155|                336|     0.427731|30004
> HI0001|SCSW-G3P1_YEAST| 1425.3|       0|            0.65868|                334|     0.648965|30000
> HI0001|ScTDH1         | 1424.6|       0|            0.65868|                334|     0.648965|30013
> HI0001|ScTDH2         | 1405.2|       0|             0.6497|                334|     0.640117|30013
> HI0001|SCSW-G3P3_YEAST| 1417.5|       0|            0.65868|                334|     0.648965|30000
> HI0001|ScTDH3         | 1416.8|       0|            0.65868|                334|     0.648965|30013
> HI0001|SCGP-3720      | 1416.8|       0|            0.66168|                334|     0.651921|30000
> HI0001|SCGP-E243731   | 1416.8|       0|            0.65868|                334|     0.648965|30000
> HI0001|SCSW-G3P2_YEAST| 1405.9|       0|             0.6497|                334|     0.640117|30000
> HI0001|SCGP-1008189   | 1424.6|       0|            0.65868|                334|     0.648965|30000
> HI0001|SCGP-3726      | 1398.7|       0|             0.6497|                334|     0.640117|30000
> HI0001|PDB3GPD_R      | 1432.2|       0|            0.63772|                334|     0.628314|30012
> HI0001|HP0921         |  762.6| 5.6e-36|            0.40407|                344|      0.41003|30005
> HI0001|MJ1146         |  124.7|     1.9|            0.25094|                267|     0.195338|30007
> HI0001|SCGP-3724      | 1371.5|       0|            0.63772|                334|     0.628314|30000
> (30 rows)
>
> real        0.18
> user        0.02
> sys         0.03
>
> QUERY: select count(*) from comparisons_4 where code = 80003
> count
> -----
>  3231
> (1 row)
>
> real        0.34
> user        0.02
> sys         0.03
>
> QUERY: select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 = 'HI0003' and c.name2 = p.name
> name   |purpose
>
-------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> MG263  |hypothetical protein
> HP0652 |phosphoserine phosphatase
> MJ1594 |phosphoserine phosphatase
> MG125  |hypothetical protein
> TP0290 |conserved hypothetical protein
> HI1033 |phosphoserine phosphatase (o-phosphoserine phosphohydrolase)
> HI0597 |hypothetical protein
> Rv3813c|(MTCY409.17), len: 273. Unknown, similar to many hypothetical proteins eg. YXEH_BACSU P54947 hypothetical
30.2kd protein in idh-deor (270 aa), fasta results; opt: 329 z-score: 456.0 E(): 2.2e-18, 32.2% identity in 267 aa
overlap
> Rv3042c|(MTV012.57c), len: 409. The C-terminal domain (150-409) is highly similar to several SerB proteins e.g.
P06862|SERB_ECOLI.N-terminus (1-150) shows no similarity, FASTA score: sp|P06862|SERB_ECOLI PHOSPHOSERINE PHOSPHATASE
(EC3.1 (322 aa) opt: 628 z-score: 753.3 E(): 0; 46.8%identity in 235 aa overlap. TBparse score is 0.884
 
> MG265  |hypothetical protein
> (10 rows)
>
> real        0.24
> user        0.02
> sys         0.03
>
> QUERY: select c.target_name, c.matched_name, c.score, p.purpose from concordance_91 c, proteins p where
c.matched_name= p.name
 
> target_name|matched_name|   score|purpose
>
-----------+------------+--------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> ECinfA     |BSInfA      |0.680556|initiation factor IF-1
> ECinfA     |HI0548      | 0.80952|initiation factor IF-1
> ECinfA     |HP1298      | 0.61111|translation initiation factor EF-1
> ECinfA     |Rv3462c     |0.684936|(MTCY13E12.15c), len: 73 aa. infA. Probable initiation factor IF-1. FASTA results:
identicalto IF1_MYCBO P45957 initiation factor if-1 (72 aa)
 
> ECrpmA     |BB0780      |0.635297|ribosomal protein L27
> ECrpmA     |HI0879      | 0.87059|ribosomal protein L27
> ECrpmA     |HP0297      |0.613632|ribosomal protein L27
> ECrpmA     |Rv2441c     |0.616278|(MTCY428.05), len: 86. Probable rpmA, similar to eg RL27_ECOLI P02427 50s ribosomal
proteinl27, (84 aa), fasta scores, opt: 328, E(): 7.1e-17, (64.2% identity in 81 aa overlap); contains PS00831
Ribosomalprotein L27 signature
 
> (8 rows)
>
> real        0.17
> user        0.02
> sys         0.03
>
>   ------------------------------------------------------------------------
> CREATE DATABASE
> CREATE TABLE "proteins" (
>         "name" character varying(16),
>         "organism" text,
>         "start_position" int4,
>         "last_position" int4,
>         "seq" text,
>         "purpose" text,
>         "alternate_key" character varying(16),
>         "comment" text,
>         "compared" bool,
>         "complement" bool,
>         "chromosome" character varying(4),
>         "essentiality" float8);
> CREATE
> COPY "proteins" FROM stdin;
> CREATE  INDEX "protein_names" on "proteins" using btree ( "name" "varchar_ops" );
> CREATE
> CREATE  INDEX "protein_organism" on "proteins" using btree ( "organism" "text_ops" );
> CREATE
>
> real     1:04.49
> user        3.14
> sys         0.57
>
> CREATE TABLE "comparisons_4" (
>         "name1" character varying(16),
>         "name2" character varying(16),
>         "z_score" float8,
>         "expected" float8,
>         "local_overlap_ratio" float8,
>         "local_overlap_count" int4,
>         "overlap_ratio" float8,
>         "code" int4);
> CREATE
> COPY "comparisons_4" FROM stdin;
> CREATE  INDEX "comparisons_4_name1" on "comparisons_4" using btree ( "name1" "varchar_ops" );
> CREATE
> CREATE  INDEX "comparisons_4_name2" on "comparisons_4" using btree ( "name2" "varchar_ops" );
> CREATE
> CREATE  INDEX "comparisons_4_code" on "comparisons_4" using btree ( "code" "int4_ops" );
> CREATE
>
> real     7:04.43
> user        5.87
> sys         1.03
>
> CREATE TABLE "concordance_91" (
>         "target_name" character varying(16),
>         "matched_name" character varying(16),
>         "score" text);
> CREATE
> REVOKE ALL on "concordance_91" from PUBLIC;
> CHANGE
> GRANT ALL on "concordance_91" to PUBLIC;
> CHANGE
> COPY "concordance_91" FROM stdin;
>
> real        0.60
> user        0.01
> sys         0.03
>
> explain select * from comparisons_4 where name1 = 'HI0001';
> NOTICE:  QUERY PLAN:
>
> Seq Scan on comparisons_4  (cost=0.00..15640.81 rows=5918 width=64)
>
> EXPLAIN
> explain select count(*) from comparisons_4 where code = 80003;
> NOTICE:  QUERY PLAN:
>
> Aggregate  (cost=15655.61..15655.61 rows=1 width=0)
>   ->  Seq Scan on comparisons_4  (cost=0.00..15640.81 rows=5918 width=0)
>
> EXPLAIN
> explain select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 = 'HI0003' and c.name2 = p.name;
> NOTICE:  QUERY PLAN:
>
> Merge Join  (cost=22495.22..23029.70 rows=2180283 width=36)
>   ->  Sort  (cost=16011.62..16011.62 rows=5918 width=12)
>         ->  Seq Scan on comparisons_4 c  (cost=0.00..15640.81 rows=5918 width=12)
>   ->  Sort  (cost=6483.60..6483.60 rows=36840 width=24)
>         ->  Seq Scan on proteins p  (cost=0.00..3247.40 rows=36840 width=24)
>
> EXPLAIN
> explain select c.target_name, c.matched_name, c.score, p.purpose from concordance_91 c, proteins p where
c.matched_name= p.name;
 
> NOTICE:  QUERY PLAN:
>
> Merge Join  (cost=6553.43..7026.43 rows=368400 width=60)
>   ->  Sort  (cost=69.83..69.83 rows=1000 width=36)
>         ->  Seq Scan on concordance_91 c  (cost=0.00..20.00 rows=1000 width=36)
>   ->  Sort  (cost=6483.60..6483.60 rows=36840 width=24)
>         ->  Seq Scan on proteins p  (cost=0.00..3247.40 rows=36840 width=24)
>
> EXPLAIN
> select * from comparisons_4 where name1 = 'HI0001'
>  name1  |      name2      | z_score | expected | local_overlap_ratio | local_overlap_count | overlap_ratio | code
> --------+-----------------+---------+----------+---------------------+---------------------+---------------+-------
>  HI0001 | PDB1GAD_O       |  1869.5 |        0 |             0.83434 |                 332 |      0.817112 | 30012
>  HI0001 | PDB1GAE_O       |  1861.8 |        0 |             0.83133 |                 332 |      0.814164 | 30012
>  HI0001 | PDB3GPD_R       |  1432.2 |        0 |             0.63772 |                 334 |      0.628314 | 30012
>  HI0001 | SCSW-G3P1_YEAST |  1425.3 |        0 |             0.65868 |                 334 |      0.648965 | 30000
>  HI0001 | SCGP-1008189    |  1424.6 |        0 |             0.65868 |                 334 |      0.648965 | 30000
>  HI0001 | ScTDH1          |  1424.6 |        0 |             0.65868 |                 334 |      0.648965 | 30013
>  HI0001 | SCSW-G3P3_YEAST |  1417.5 |        0 |             0.65868 |                 334 |      0.648965 | 30000
>  HI0001 | ScTDH3          |  1416.8 |        0 |             0.65868 |                 334 |      0.648965 | 30013
>  HI0001 | SCGP-3720       |  1416.8 |        0 |             0.66168 |                 334 |      0.651921 | 30000
>  HI0001 | SCGP-E243731    |  1416.8 |        0 |             0.65868 |                 334 |      0.648965 | 30000
>  HI0001 | SCSW-G3P2_YEAST |  1405.9 |        0 |              0.6497 |                 334 |      0.640117 | 30000
>  HI0001 | ScTDH2          |  1405.2 |        0 |              0.6497 |                 334 |      0.640117 | 30013
>  HI0001 | SCPIR-DEBYG1    |  1405.2 |        0 |              0.6497 |                 334 |      0.640117 | 30000
>  HI0001 | SCGP-3726       |  1398.7 |        0 |              0.6497 |                 334 |      0.640117 | 30000
>  HI0001 | SCGP-3724       |  1371.5 |        0 |             0.63772 |                 334 |      0.628314 | 30000
>  HI0001 | PDB4GPD_1       |  1357.8 |        0 |             0.64865 |                 333 |      0.637169 | 30012
>  HI0001 | PDB2GD1_P       |  1226.4 |        0 |             0.57015 |                 335 |      0.563423 | 30012
>  HI0001 | PDB2DBV_O       |  1217.4 |        0 |             0.56716 |                 335 |      0.560468 | 30012
>  HI0001 | PDB4DBV_O       |    1207 |        0 |             0.56418 |                 335 |      0.557523 | 30012
>  HI0001 | PDB1HDG_O       |  1020.4 |        0 |             0.48024 |                 329 |      0.466074 | 30012
>  HI0001 | Rv1436          |   970.4 |        0 |             0.49558 |                 339 |       0.49558 | 30010
>  HI0001 | PDB1CER_O       |   949.7 |        0 |             0.47734 |                 331 |      0.466075 | 30012
>  HI0001 | PDB1NLH_        |   935.1 |        0 |             0.46847 |                 333 |      0.458825 | 30012
>  HI0001 | PDB1GGA_A       |     918 |        0 |             0.52125 |                 353 |       0.51397 | 30012
>  HI0001 | PDB1GYP_A       |   900.1 |        0 |             0.51275 |                 353 |      0.505589 | 30012
>  HI0001 | MG301           |   866.7 |        0 |             0.43155 |                 336 |      0.427731 | 30004
>  HI0001 | HP1346          |   850.3 |  6.9e-41 |             0.39222 |                 334 |      0.386435 | 30005
>  HI0001 | TP0844          |   780.3 |  5.8e-37 |             0.46307 |                 352 |      0.465716 | 30014
>  HI0001 | HP0921          |   762.6 |  5.6e-36 |             0.40407 |                 344 |       0.41003 | 30005
>  HI0001 | MJ1146          |   124.7 |      1.9 |             0.25094 |                 267 |      0.195338 | 30007
> (30 rows)
>
> real       22.68
> user        0.01
> sys         0.03
>
> select count(*) from comparisons_4 where code = 80003
>  count
> -------
>   3231
> (1 row)
>
> real       21.49
> user        0.01
> sys         0.03
>
> select p.name, p.purpose from comparisons_4 c, proteins p where c.name1 = 'HI0003' and c.name2 = p.name
>   name   |
                                                    purpose
 
>
---------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>  HI0597  | hypothetical protein
>  HI1033  | phosphoserine phosphatase (o-phosphoserine phosphohydrolase)
>  HP0652  | phosphoserine phosphatase
>  MG125   | hypothetical protein
>  MG263   | hypothetical protein
>  MG265   | hypothetical protein
>  MJ1594  | phosphoserine phosphatase
>  Rv3042c | (MTV012.57c), len: 409. The C-terminal domain (150-409) is highly similar to several SerB proteins e.g.
P06862|SERB_ECOLI.N-terminus (1-150) shows no similarity, FASTA score: sp|P06862|SERB_ECOLI PHOSPHOSERINE PHOSPHATASE
(EC3.1 (322 aa) opt: 628 z-score: 753.3 E(): 0; 46.8%identity in 235 aa overlap. TBparse score is 0.884 
>  Rv3813c | (MTCY409.17), len: 273. Unknown, similar to many hypothetical proteins eg. YXEH_BACSU P54947 hypothetical
30.2kd protein in idh-deor (270 aa), fasta results; opt: 329 z-score: 456.0 E(): 2.2e-18, 32.2% identity in 267 aa
overlap
>  TP0290  | conserved hypothetical protein
> (10 rows)
>
> real       23.13
> user        0.01
> sys         0.03
>
> select c.target_name, c.matched_name, c.score, p.purpose from concordance_91 c, proteins p where c.matched_name =
p.name
>  target_name | matched_name |  score   |
                                purpose
 
>
-------------+--------------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>  ECrpmA      | BB0780       | 0.635297 | ribosomal protein L27
>  ECinfA      | BSInfA       | 0.680556 | initiation factor IF-1
>  ECinfA      | HI0548       | 0.80952  | initiation factor IF-1
>  ECrpmA      | HI0879       | 0.87059  | ribosomal protein L27
>  ECrpmA      | HP0297       | 0.613632 | ribosomal protein L27
>  ECinfA      | HP1298       | 0.61111  | translation initiation factor EF-1
>  ECrpmA      | Rv2441c      | 0.616278 | (MTCY428.05), len: 86. Probable rpmA, similar to eg RL27_ECOLI P02427 50s
ribosomalprotein l27, (84 aa), fasta scores, opt: 328, E(): 7.1e-17, (64.2% identity in 81 aa overlap); contains
PS00831Ribosomal protein L27 signature
 
>  ECinfA      | Rv3462c      | 0.684936 | (MTCY13E12.15c), len: 73 aa. infA. Probable initiation factor IF-1. FASTA
results:identical to IF1_MYCBO P45957 initiation factor if-1 (72 aa)
 
> (8 rows)
>
> real       11.16
> user        0.01
> sys         0.03